ozarki,
I am not sure what the maximum file size for the .ini is. I think it is like 64 MB.
I have several small scripts in my AHK.ini, but then I also have stand alone scripts just to keep everything organized. The ones that deal with macros are in one. The ones that deal with physician paragraph templates are in another, and the ones that deal with dates, blood pressure, ages, etc are in another. And then I also have the hotstrings in another.
I didn't like having a lot of icons in the taskbar, so I added #NoTrayIcon to a lot of them. I keep those in my Quick Launch folder so I have easy access to them. I also assigned a universal “reload” hotkey to restart all my scripts without having to use the mouse. For the most part, once I get used to using a script, I get rid of the tray icon. The only icons I have showing are the hotstrings scripts.
I am sure everyone has their own way of keeping scripts. With time, you will find something that works for you. I would be interested in hearing how others do it.

Grabber